Narrow escape: how ionizing photons escape from disc galaxies

In this paper we calculate the escape fraction (f(esc)) of ionizing photons from starburst galaxies. Using 2D axisymmetric hydrodynamic simulations, we study superbubbles created by overlapping supernovae in OB associations. We calculate the escape fraction of ionizing photons from the centre of the disc along different angles through the superbubble and the gas disc. After convolving with the luminosity function of OB associations, we show that the ionizing photons escape within a cone of similar to 40 degrees, consistent with observations of nearby galaxies. The evolution of the escape fraction with time shows that it falls initially as cold gas is accumulated in a dense shell. After the shell crosses a few scaleheights and fragments, the escape fraction through the polar regions rises again. The angle-averaged escape fraction cannot exceed similar to1 - cos (1 rad)] = 0.5 from geometrical considerations (using the emission cone opening angle). We calculate the dependence of the time-and angle-averaged escape fraction on the mid-plane disc gas density (in the range n(0) = 0.15-50 cm(-3)) and the disc scaleheight (between z(0) = 10 and 600 pc). We find that the escape fraction is related to the disc parameters (the mid-plane disc density and scaleheight) roughly so that f(esc)(alpha)n(0)(2)z(0)(3) (with alpha approximate to 2.2) is a constant. For discs with a given warm neutral medium temperature, massive discs have lower escape fraction than low-mass galaxies. For Milky Way ISM parameters, we find f(esc) similar to 5 per cent, and it increases to approximate to 10 per cent for a galaxy 10 times less massive. We discuss the possible effects of clumpiness of the ISM on the estimate of the escape fraction and the implications of our results for the reionization of the Universe.

Anomalous reaction-diffusion as a model of nonexponential DNA escape kinetics

We show that data from recent experiments carried out on the kinetics of DNA escape from alpha-hemolysin nanopores [M. Wiggin, C. Tropini, C. T. Cossa, N. N. Jetha, and A. Marziali, Biophys. J. 95, 5317 (2008)] may be rationalized by a model of chain dynamics based on the anomalous diffusion of a particle moving in a harmonic well in the presence of a delta function sink. The experiments of Wiggin found, among other things, that the occasional occurrence of unusually long escape times in the distribution of chain trapping events led to nonexponential decays in the survival probability, S(t), of the DNA molecules within the nanopore. Wiggin ascribed this nonexponentiality to the existence of a distribution of trapping potentials, which they suggested was theresult of stochastic interactions between the bases of the DNA and the amino acids located on the surface of the nanopore. Based on this idea, they showed that the experimentally determined S(t) could be well fit in both the short and long time regimes by a function of the form (1+t/tau)(-alpha) (the so called Becquerel function). In our model, S(t) is found to be given by a Mittag-Leffler function at short times and by a generalized Mittag-Leffler function at long times. By suitable choice of certain parameter values, these functions are found to fit the experimental S(t) even better than the Becquerel function. Anomalous diffusion of DNA within the trap prior to escape over a barrier of fixed height may therefore provide a second, plausible explanation of the data, and may offer fresh perspectives on similar trapping and escape problems.

Hemagglutinin sequence conservation guided stem immunogen design from influenza A H3 subtype

Seasonal epidemics caused by influenza A (H1 and H3 subtypes) and B viruses are a major global health threat. The traditional, trivalent influenza vaccines have limited efficacy because of rapid antigenic evolution of the circulating viruses. This antigenic variability mediates viral escape from the host immune responses, necessitating annual vaccine updates. Influenza vaccines elicit a protective antibody response, primarily targeting the viral surface glycoprotein hemagglutinin (HA). However, the predominant humoral response is against the hypervariable head domain of HA, thereby restricting the breadth of protection. In contrast, the conserved, subdominant stem domain of HA is a potential ``universal'' vaccine candidate. We designed an HA stem-fragment immunogen from the 1968 pandemic H3N2 strain (A/Hong Kong/1/68) guided by a comprehensive H3 HA sequence conservation analysis. The biophysical properties of the designed immunogen were further improved by C-terminal fusion of a trimerization motif, ``isoleucine-zipper'', or ``foldon''. These immunogens elicited cross-reactive, antiviral antibodies and conferred partial protection against a lethal, homologous HK68 virus challenge in vivo. Furthermore, bacterial expression of these immunogens is economical and facilitates rapid scale-up.

Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1

Following transmission, HIV-1 adapts in the new host by acquiring mutations that allow it to escape from the host immune response at multiple epitopes. It also reverts mutations associated with epitopes targeted in the transmitting host but not in the new host. Moreover, escape mutations are often associated with additional compensatory mutations that partially recover fitness costs. It is unclear whether recombination expedites this process of multi-locus adaptation. To elucidate the role of recombination, we constructed a detailed population dynamics model that integrates viral dynamics, host immune response at multiple epitopes through cytotoxic T lymphocytes, and viral evolution driven by mutation, recombination, and selection. Using this model, we compute the expected waiting time until the emergence of the strain that has gained escape and compensatory mutations against the new host's immune response, and reverted these mutations at epitopes no longer targeted. We find that depending on the underlying fitness landscape, shaped by both costs and benefits of mutations, adaptation proceeds via distinct dominant pathways with different effects of recombination, in particular distinguishing escape and reversion. When adaptation at a single epitope is involved, recombination can substantially accelerate immune escape but minimally affects reversion. When multiple epitopes are involved, recombination can accelerate or inhibit adaptation depending on the fitness landscape. Specifically, recombination tends to delay adaptation when a purely uphill fitness landscape is accessible at each epitope, and accelerate it when a fitness valley is associated with each epitope. Our study points to the importance of recombination in shaping the adaptation of HIV-1 following its transmission to new hosts, a process central to T cell-based vaccine strategies. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license.

Barrier crossing in one and three dimensions by a long chain

We consider the Kramers problem for a long chain polymer trapped in a biased double-well potential. Initially the polymer is in the less stable well and it can escape from this well to the other well by the motion of its N beads across the barrier to attain the configuration having lower free energy. In one dimension we simulate the crossing and show that the results are in agreement with the kink mechanism suggested earlier. In three dimensions, it has not been possible to get an analytical `kink solution' for an arbitrary potential; however, one can assume the form of the solution of the nonlinear equation as a kink solution and then find a double-well potential in three dimensions. To verify the kink mechanism, simulations of the dynamics of a discrete Rouse polymer model in a double well in three dimensions are carried out. We find that the time of crossing is proportional to the chain length, which is in agreement with the results for the kink mechanism. The shape of the kink solution is also in agreement with the analytical solution in both one and three dimensions.

Salmonella enterica serovars Typhimurium and Typhi as model organisms Revealing paradigm of host-pathogen interactions

The lifestyle of intracellular pathogens has always questioned the skill of a microbiologist in the context of finding the permanent cure to the diseases caused by them. The best tool utilized by these pathogens is their ability to reside inside the host cell, which enables them to easily bypass the humoral immunity of the host, such as the complement system. They further escape from the intracellular immunity, such as lysosome and inflammasome, mostly by forming a protective vacuole-bound niche derived from the host itself. Some of the most dreadful diseases are caused by these vacuolar pathogens, for example, tuberculosis by Mycobacterium or typhoid fever by Salmonella. To deal with such successful pathogens therapeutically, the knowledge of a host-pathogen interaction system becomes primarily essential, which further depends on the use of a model system. A well characterized pathogen, namely Salmonella, suits the role of a model for this purpose, which can infect a wide array of hosts causing a variety of diseases. This review focuses on various such aspects of research on Salmonella which are useful for studying the pathogenesis of other intracellular pathogens.

Development of micro-shock wave assisted dry particle and fluid jet delivery system

Small quantity of energetic material coated on the inner wall of a polymer tube is proposed as a new method to generate micro-shock waves in the laboratory. These micro-shock waves have been harnessed to develop a novel method of delivering dry particle and liquid jet into the target. We have generated micro-shock waves with the help of reactive explosive compound high melting explosive (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) and traces of aluminium] coated polymer tube, utilising 9 J of energy. The detonation process is initiated electrically from one end of the tube, while the micro-shock wave followed by the products of detonation escape from the open end of the polymer tube. The energy available at the open end of the polymer tube is used to accelerate tungsten micro-particles coated on the other side of the diaphragm or force a liquid jet out of a small cavity filled with the liquid. The micro-particles deposited on a thin metal diaphragm (typically 100-mu m thick) were accelerated to high velocity using micro-shock waves to penetrate the target. Tungsten particles of 0.7 mu m diameter have been successfully delivered into agarose gel targets of various strengths (0.6-1.0 %). The device has been tested by delivering micro-particles into potato tuber and Arachis hypogaea Linnaeus (ground nut) stem tissue. Along similar lines, liquid jets of diameter 200-250 mu m (methylene blue, water and oils) have been successfully delivered into agarose gel targets of various strengths. Successful vaccination against murine salmonellosis was demonstrated as a biological application of this device. The penetration depths achieved in the experimental targets are very encouraging to develop a future device for biological and biomedical applications.

Corporate social responsibilities of Indian public sector enterprises-a case study of Bharat Heavy Electricals Limited (BHEL)

The high level of public accountability attached to Public Sector Enterprises as a result of public ownership makes them socially responsible. The Committee of Public Undertakings in 1992 examined the issue relating to social obligations of Central Public Sector Enterprises and observed that ``being part of the `State', every Public Sector enterprise has a moral responsibility to play an active role in discharging the social obligations endowed on a welfare state, subject to the financial health of the enterprise''. It issued the Corporate Social Responsibility Guidelines in 2010 where all Central Public Enterprises, through a Board Resolution, are mandated to create a CSR budget as a specified percentage of net profit of the previous year. This paper examines the CSR activities of the biggest engineering public sector organization in India, Bharath Heavy Electricals Limited. The objectives are twofold, one, to develop a case study of the organization about the funds allocated and utilized for various CSR activities, and two, to examine its status with regard to other organizations, the 2010 guidelines, and the local socio-economic development. Secondary data analysis results show three interesting trends. One, it reveals increasing organizational social orientation with the formal guidelines in place. Two, Firms can no longer continue to exploit environmental resources and escape from their responsibilities by acting separate entities regardless of the interest of the society and Three the thrust of CSR in public sector is on inclusive growth, sustainable development and capacity building with due attention to the socio-economic needs of the neglected and marginalized sections of the society.

Exciton-phonon scattering and nonradiative relaxation of excited carriers in hydrothermally synthesized CdTe quantum dots

Naturally formed CdTe/CdS core/shell quantum dot (QD) structures in the presence of surface stabilizing agents have been synthesized by a hydrothermal method. Size and temperature dependent photoluminescence (PL) spectra have been investigated to understand the exciton-phonon interaction, and radiative and nonradiative relaxation of carriers in these QDs. The PL of these aqueous CdTe QDs (3.0-4.8 nm) has been studied in the temperature range 15-300 K. The strength of the exciton-LO-phonon coupling, as reflected in the Huang-Rhys parameter `S' is found to increase from 1.13 to 1.51 with the QD size varying from 4.8 to 3.0 nm. The PL linewidth (FWHM) increases with increase in temperature and is found to have a maximum in the case of QDs of 3.0 nm in size, where the exciton-acoustic phonon coupling coefficient is enhanced to 51 mu eV K-1, compared to the bulk value of 0.72 mu eV K-1. To understand the nonradiative processes, which affect the relaxation of carriers, the integrated PL intensity is observed as a function of temperature. The integrated PL intensity remains constant until 50 K for relatively large QDs (3.9-4.8 nm) beyond which a thermally activated process takes over. Below 150 K, a small activation energy, 45-19 meV, is found to be responsible for the quenching of the PL. Above 150 K, the thermal escape from the dot assisted by scattering with multiple longitudinal optical (LO) phonons is the main mechanism for the fast quenching of the PL. Besides this high temperature quenching, interestingly for relatively smaller size QDs (3.4-3.0 nm), the PL intensity enhances as the temperature increases up to 90-130 K, which is attributed to the emission of carriers from interface/trap states having an activation energy in the range of 6-13 meV.

Polyketide Quinones Are Alternate Intermediate Electron Carriers during Mycobacterial Respiration in Oxygen-Deficient Niches

Mycobacterium tuberculosis (Mtb) adaptation to hypoxia is considered crucial to its prolonged latent persistence in humans. Mtb lesions are known to contain physiologically heterogeneous microenvironments that bring about differential responses from bacteria. Here we exploit metabolic variability within biofilm cells to identify alternate respiratory polyketide quinones (PkQs) from both Mycobacterium smegmatis (Msmeg) and Mtb. PkQs are specifically expressed in biofilms and other oxygen-deficient niches to maintain cellular bioenergetics. Under such conditions, these metabolites function as mobile electron carriers in the respiratory electron transport chain. In the absence of PkQs, mycobacteria escape from the hypoxic core of biofilms and prefer oxygenrich conditions. Unlike the ubiquitous isoprenoid pathway for the biosynthesis of respiratory quinones, PkQs are produced by type III polyketide synthases using fatty acyl-CoA precursors. The biosynthetic pathway is conserved in several other bacterial genomes, and our study reveals a redox-balancing chemicocellular process in microbial physiology.

Characterization of silver-kaolinite (AgK): an adsorbent for long-lived I-129 species

Bentonite is a preferred buffer and backfill material for deep geological disposal of high-level nuclear waste (HLW). Bentonite does not retain anions by virtue of its negatively charged basal surface. Imparting anion retention ability to bentonite is important to enable the expansive clay to retain long-lived I-129 (iodine-129; half-life = 16 million years) species that may escape from the HLW geological repository. Silver-kaolinite (AgK) material is prepared as an additive to improve the iodide retention capacity of bentonite. The AgK is prepared by heating kaolinite-silver nitrate mix at 400 degrees C to study the kaolinite influence on the transition metal ion when reacting at its dehydroxylation temperature. Thermo gravimetric-Evolved Gas Detection analysis, X-ray diffraction analysis, X-ray photo electron spectroscopy and electron probe micro analysis indicated that silver occurs as AgO/Ag2O surface coating on thermally reacting kaolinite with silver nitrate at 400 degrees C.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Electrical Characterization of Airborne Vehicle Exhaust Plume

he induced current and voltage on the skin of an airborne vehicle due to the coupling of external electromagnetic field could be altered in the presence of ionized exhaust plume. So in the present work, a theoretical analysis is done to estimate the electrical parameters such as electrical conductivity and permittivity and their distribution in the axial and radial directions of the exhaust plume of an airborne vehicle. The electrical conductivity depends on the distribution of the major ionic species produced from the propellant combustion. In addition it also depends on temperature and pressure distribution of the exhaust plume as well as the generated shock wave. The chemically reactive rocket exhaust flow is modeled in two stages. The first part is simulated from the combustion chamber to the throat of the supersonic nozzle by using NASA Chemical Equilibrium with Application (CEA) package and the second part is simulated from the nozzle throat to the downstream of the plume by using a commercial Computational Fluid Dynamics (CFD) solver. The contour plots of the exhaust parameters are presented. Eight barrel shocks which influence the distribution of the vehicle exhaust parameters are obtained in this simulation. The computed peak value of the electrical conductivity of the plume is 0.123 S/m and the relative permittivity varies from 0.89 to 0.99. The attenuation of the microwave when it is passing through the conducting exhaust plume has also been presented.

A Modified Dubins Method for Optimal Path Planning of a Miniature Air Vehicle Converging to a Straight Line Path

This paper presents a Dubins model based strategy to determine the optimal path of a Miniature Air Vehicle (MAV), constrained by a bounded turning rate, that would enable it to fly along a given straight line, starting from an arbitrary initial position and orientation. The method is then extended to meet the same objective in the presence of wind which has a magnitude comparable to the speed of the MAV. We use a modification of the Dubins' path method to obtain the complete optimal solution to this problem in all its generality.

Vehicle Routing Problem with Load Compatibility Constraints

The major contribution of this paper is to introduce load compatibility constraints in the mathematical model for the capacitated vehicle routing problem with pickup and deliveries. The employee transportation problem in the Indian call centers and transportation of hazardous materials provided the motivation for this variation. In this paper we develop a integer programming model for the vehicle routing problem with load compatibility constraints. Specifically two types of load compatability constraints are introduced, namely mutual exclusion and conditional exclusion. The model is demonstrated with an application from the employee transportation problem in the Indian call centers.